A comparative evaluation of dynamic visualisation tools

Despite their potential applications in software comprehension, it appears that dynamic visualisation tools are seldom used outside the research laboratory. This paper presents an empirical evaluation of five dynamic visualisation tools - AVID, Jinsight, jRMTool, Together ControlCenter diagrams and Together ControlCenter debugger. The tools were evaluated on a number of general software comprehension and specific reverse engineering tasks using the HotDraw objectoriented framework. The tasks considered typical comprehension issues, including identification of software structure and behaviour, design pattern extraction, extensibility potential, maintenance issues, functionality location, and runtime load. The results revealed that the level of abstraction employed by a tool affects its success in different tasks, and that tools were more successful in addressing specific reverse engineering tasks than general software comprehension activities. It was found that no one tool performs well in all tasks, and some tasks were beyond the capabilities of all five tools. This paper concludes with suggestions for improving the efficacy of such tools

The geography of religious affiliation in Glasgow

The geography of religion has received limited research attention within cultural geography in the UK. The present research employs a statistical-cartographic approach to provide a detailed mapping of the geography of religious affiliation in Glasgow. The paper first addresses a number of key conceptual and methodological questions underlying the mapping of geographies of religion; then presents a detailed empirical analysis of different socio-cultural, spatial and temporal dimensions of the geography of religious affiliation in the city. Finally, based on the findings of the present research, a number of questions for further research are identified

Endothelin-2-Mediated Protection of Mutant Photoreceptors in Inherited Photoreceptor Degeneration

<div><p>Expression of the <i>Endothelin-2 (Edn2)</i> mRNA is greatly increased in the photoreceptors (PRs) of mouse models of inherited PR degeneration (IPD). To examine the role of <i>Edn2</i> in mutant PR survival, we generated <i>Edn2^−/−</i> mice carrying homozygous <i>Pde6b^rd1</i> alleles or the <i>Tg(RHO P347S)</i> transgene. In the <i>Edn2^−/−</i> background, PR survival increased 110% in <i>Pde6b^rd1/rd1</i> mice at post-natal (PN) day 15, and 60% in <i>Tg(RHO P347S)</i> mice at PN40. In contrast, PR survival was not increased in retinal explants of <i>Pde6b^rd1/rd1</i>; <i>Edn2^−/−</i> mice. This finding, together with systemic abnormalities in <i>Edn2^−/−</i> mice, suggested that the increased survival of mutant PRs in the <i>Edn2^−/−</i> background resulted at least partly from the systemic EDN2 loss of function. To examine directly the role of EDN2 in mutant PRs, we used a scAAV5-<i>Edn2</i> cDNA vector to restore <i>Edn2</i> expression in <i>Pde6b^rd1/rd1</i>; <i>Edn2^−/−</i> PRs and observed an 18% increase in PR survival at PN14. Importantly, PR survival was also increased after injection of scAAV5-<i>Edn2</i> into <i>Pde6b^rd1/rd1</i> retinas, by 31% at PN15. Together, these findings suggest that increased <i>Edn2</i> expression is protective to mutant PRs. To begin to elucidate <i>Edn2</i>-mediated mechanisms that contribute to PR survival, we used microarray analysis and identified a cohort of 20 genes with >4-fold increased expression in <i>Tg(RHO P347S)</i> retinas, including <i>Fgf2</i>. Notably, increased expression of the FGF2 protein in <i>Tg(RHO P347S)</i> PRs was ablated in <i>Tg(RHO P347S)</i>; <i>Edn2^−/−</i> retinas. Our findings indicate that the increased expression of PR <i>Edn2</i> increases PR survival, and suggest that the <i>Edn2</i>-dependent increase in PR expression of FGF2 may contribute to the augmented survival.</p> </div

Expression of GFP and <i>Edn2</i> from subretinally injected scAAV5.

<p>(A) The temporal and spatial expression of GFP in WT retinas injected subretinally with 1X PBS or scAAV5-smCBA-<i>Gfp</i> at PN8 and evaluated at PN10, PN12, and PN14 by GFP immunofluorescence (A, Panels 1–4). Significant GFP staining was not observed until PN12, with stronger staining at PN14, especially in the vicinity of the subretinal injection site (arrow). The spatial expression of GFP in WT retinas injected with scAAV5-smCBA-<i>Gfp</i> was also evaluated in paraffin sections at PN12 (A, Panel 5). GFP expression was observed predominantly in the ONL and RPE; sporadic expression of GFP in Müller cells was also observed in paraffin sections. (Bar = 25 µm.) (B) Schematic of the EDN2 cleavage events required to produce the mature EDN2 peptide. EDN2 is first produced as prepro EDN2 (175 aa) which is rapidly processed by furin-like endopeptidases to yield big EDN2 (38 aa). Big EDN2 must then be cleaved by an endothelin-specific converting enzyme (ECE) to produce the 21 a.a. mature EDN2 peptide that can bind to endothelin receptors (figure adapted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058023#pone.0058023-Saida1" target="_blank">[68]</a>). The regions of the <i>Edn2</i> mRNA corresponding to the cDNAs cloned into the scAAV5-<i>smCBA</i>-prepro<i>Edn2</i> and scAAV5-<i>smCBA</i>-mat<i>Edn2</i> vectors are shown. (C) Expression of scAAV5-derived <i>Edn2</i> mRNA in <i>Pde6b^rd1/rd1</i> retinas at PN12 after injection of the scAAV5-<i>smCBA</i>-prepro<i>Edn2</i> and scAAV5-<i>smCBA</i>-mat<i>Edn2</i> constructs at PN8. scAAV5-derived <i>Edn2</i> mRNA expression values are shown relative to the levels of endogenous <i>Edn2</i> mRNA (from the same retina) and all values were normalized to <i>Gapdh</i>. scAAV5-prepro<i>Edn2</i> transcripts were increased between 1.7 and 7.2-fold (n = 4; average 4.3-fold) over endogenous <i>Edn2</i> mRNA, while scAAV5-mat<i>Edn2</i> transcripts increased between 2.5 to 11.3-fold over the endogenous <i>Edn2</i> mRNA (n = 4; average 6.9-fold). ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer. Error bars indicate SEM.</p